I think it makes a difference in the application of H1B - as "toosad" said, you get an extra chance if the lottery has to be carried out.
For green card purposes, it depends on the job you'll get after your degree. If the job description calls for a master's degree, you'll most likely file the green card application under EB2. If the job only requires a bachelor's degree, your master's wouldn't help since any qualified American citizen with a bachelor's would theoretically be able to do your job.
Good luck.